And War Erupts
by Totopup
Summary: Sequel to 'A daughter for Sherlock' so you should probably check that out first, but you can catch on if you clever... Sherlock discovers his human side and his love for Samantha as Moriarty wreaks havoc in Sherlocks world.
1. Chapter 1

**1 Year Later**

The battle to unite the two families was going... Let's just say OK. At least neither Samantha or Sherlock had been hurt, and John was still as... Well... Johnny as ever. Sherlock hadn't seen Sam for 3 months but he was OK with that. She was probably off following up a lead or something.

Sherlock felt his phone vibrate in his pocket. He took his time, and he knew exactly how many rings there were anyway, so there was no rush.

"Hello." he said calmly, and was surprised to hear no response for a second. Then he heard a desperate whisper, a voice he recognised all too well.

"God, Sherlock they're here. The Sanders. They're here." he heard a scuffling sound and a smash, then a heavy thud.

"Sam? What's happening?" Sherlock asked, sitting up, and for the first time in his life felt a sharp pang of hurt in his heart. They had gone after Sam.

"Shit Sherlock, they're here! Oh God, h-" she cut off and he heard a scream, muffled as though her mouth was pressed up against something.

"**_JOHN!_**" Sherlock screamed through the house, and John appeared a second later, wearing a black suit having just come home from work. He had filled John in with all the details about Samantha 1 year ago.

"Call Mycroft and Lestrade. Tell Mrs Hudson I will be back late." John gave him a confused look.

"They have Sam."

John jumped into action as Sherlock pressed the phone to his ear again. No sobbing, just short, terrified breaths.

"Sam, I'm coming. Don't cut off the phone line. Don't." Sherlock said into the phone in the calmest voice he could muster, not bothering with a coat or scarf, just forcing his feet into his boots.

"Who else have you called?" Sherlock asked her, trying to keep the panic out of his voice as he heard many more smashes and thuds. He raced down the stairs, out the door and straight in front of a taxi which abruptly stopped and let him in.

"No one, you were the only person I could think of." she whispered down the phone.

Sherlock yelled at the taxi to take him to Sam's house. He kept talking to Sam on the phone, trying to calm her down. He wasn't much good at it.

"And remember when-" he was cut off by a loud, hurtful scream, then static. The phone had been cut off. Sherlock was seriously worried now, and screamed at the cabbie to drive faster.

Eventually he got to her flat, walking in the front door (whoever came after her had left the door open). There was a series of heavy thuds from inside, and a groan.

"Sam? I'm coming." Sherlock yelled through the house and ran into the room where the noises were coming from.

There were three men with metal batons and knives inside, clad in black. They took one look at Sherlock and scarpered, running out the door for all they were worth. Another thing – they had Samantha.


	2. Chapter 2

Sherlock screamed. He yelled and moaned and groaned and screamed and screamed and screamed. He collapsed into a teary wreck then screamed again. This was the state John and Lestrade had found him in, knelt yelling on the floor. The closest thing he had ever had to a family (apart from John) had been ruthlessly taken from him, and Sherlock's humanity was starting to show through.  
>He stood up and with watery and terrified eyes stared at John like he wasn't there. He looked like he was about to say something but faltered.<br>"I... John... She's gone. They t-took her." he stammered, standing but eventually looking like he was going to fall over, so John held the taller man up, holding him like a distraught child. I guess he was in some ways.  
>"It's OK Sherlock... We'll get her back..." John promised to him and gave Lestrade a look which clearly said 'Tell Myroft what happened NOW.'. Sherlock continued to moan until his voice went hoarse.<br>"She'll be OK Sherlock." John said as they got into the back of a police car, Sherlock resting his head on John's shoulder. Sherlock shook his head.  
>"The Sanders have got her." his voice broke, and he stopped a second before carrying on.<br>"If she's still alive now I'd be surprised. They would have probably cut a limb off or something, then send me a photo to..." he trailed off, not wanting to think about what a photo like that would do to him. He was already screaming on the inside, wanting to rip himself apart, and find the part of him that cared to mute it. To rid himself of pain. He had been so stupid, just letting her go off like that. She wouldn't have fought back. She was a pacifist.  
>The cab pulled up outside 221b Baker Street, and John got out, pulling Sherlock with him. Sherlock followed steadily, like a dog following his master. His eyes were vacant, his facial expression... Not there. Simply not there. John guessed Sherlock had gone into 'Overly autistic can't cope with anything' mode.<br>John opened the flat door and Sherlock followed him inside, instantly lying down on the sofa and not breathing a word. John asked if Sherlock wanted him to stay. He didn't reply, so John went up to his room and spent the night alone, still in awe of the human side of Sherlock. He just... Well. Sherlock had always seemed unattached. Harsh. Brittle. And then all of a sudden John walks in on a shivering wreck of a man, screaming like he had just been stabbed in the chest. It wasn't right.

John woke the next morning to silence. There was no sound. Probably what had woken him.  
>As he put his dressing gown on and walked down the stairs he heard muffled talking from the flat.<br>"Sherlock, there is clear signs she is still alive. No drag marks from her flat. CCTV shows her being walked out of the house into a white van and driven away. Then there's the text you received-" at this point John walked into the room, interrupting Mycroft. Both him and Sherlock looked up, surprised.  
>"What text?" John demanded. Mycroft took the phone from Sherlock and gave it to John.<br>On the screen there was a clear picture of Sam lying in a dark room, clearly drugged. She was covered in bruises and cuts and from the longest gash John had ever seen running down her back and the back of her left leg was gushing blood, soaking her clothes, hands and feet. There was a dark figure standing behind her. John couldn't quite make out who it was.  
>"Oh my God. Sherlock..." John started, but Mycroft gave John a look. He shut up.<p>

Sherlock moaned, covering his face with his hands. Mycroft looked on, slightly amused.  
>"Can you find her?" Sherlock asked in a cracked voice. He was taking it all a bit hard, John thought. Like Sam had actually died.<br>"We already have a list of possible places she could be. I have my best men crossing off the impossible and will come to me shortly with a shortlist." explained Mycroft. Sherlock sat bolt upright.  
>"Shouldn't I be doing that?" Sherlock demanded. Mycroft looked at him like 'really?'.<br>"Well, I don't trust you're judgement at the moment." Mycroft said boldly, and Sherlock relaxed again.  
>Mycroft left, promising to come right away when the shortlist was put together. John managed to persuade Sherlock to get dressed, shave and wash, but he wouldn't eat anything. Not a single bite.<br>"Aren't you hungry Sherlock?" he asked. Sherlock just grunted, then lay back down on the sofa, moaning and groaning softly and occasionally crying at his 'loss'. What John couldn't understand was why Sherlock was so upset.  
>"Sherlock, she's still alive. In the picture, she was still alive. Why are you so..." John asked. Sherlock just looked at him.<br>"She's held captive by the Sanders, she's as good as dead." Sherlock whispered, then turned his back and resumed his state of despair. John felt sorry for him. He had lost one of the very few things that mattered to him, and now he was taunted by the people who did it. Anyone would go mad.  
>No word from Mycroft until the next morning. Sherlock had slept right through to 11, and John had watched him, as peaceful as a baby, face devoid of all emotion, at last away from his mad despair. John hadn't been keen to wake him, but Sherlock would kill him if he didn't, so when Mycroft arrived he gently shook the disturbed man awake to listen to Mycroft.<br>"So. 5 places she could be. 1. Block of flats near suffolk, owned by the Sanders family and out of use for about 3 years." he said and waited for Sherlock to say something.  
>"No. Too far away."<br>"2. House in east London, owned by one of the general's and occasionally used by the Sanders for the storage of illegal drugs and other substances."  
>"No. Too obvious."<br>"3. Abandoned warehouse on the outskirts of north London, occasionally used by them for storage, but otherwise unused."  
>This time Sherlock smiled. <p>


	3. Chapter 3

Sherlock had received two more texts with pictures of Sam in. The first had been a picture of her standing up and trying to walk but screaming with pain from the gash, and the second was of a man mercilessly hitting her stomach. Sherlock had gone mad at this, lying on the sofa and not talking for days as the operation was put in place, groaning and moaning and not eating.  
>John noticed he was looking thin, and his breathing was ragged, so he had almost literally forced Sherlock to eat Chinese, but in the end Sherlock found himself eating by himself, starved. He looked better now, John noted.<br>There was a phone call from Mycroft telling John to make Sherlock presentable and meet him and the rest of the team by the sandwich bar beside the house.  
>20 minutes later, John and Sherlock walked out of the house and met with Mycroft, Lestrade and a few SWAT team people. They got into cars and vans and drove off. The briefing was short, and they got there in less than an hour.<br>Sherlock was nervous. He was already terrified to his wits end at the fact that Sam could die. That was part of the fact why Sherlock had been moaning the past few days. He was scared. He had to get to Sam, hold her, tell her it would be OK, tell her he... Loved her. Tell her he's sorry for not saying so before, and that he wants her to move in with him and John, and that he wants to- needs to- help her fight the war against the Sanders and Holmes', tell her that he wasn't sure quite how he could ever live without her, how she scared the death out of him when they did that, how he needed her...  
>"OK team, go." the SWAT team and Lestrade went into the warehouse, and sounds of gunfire erupted. Thuds ensued and he heard a scream.<br>John jumped out of the car and Sherlock followed. Mycroft was to stay inside the car. Sherlock took a deep breath. Then sighed. Then let his heart take over his head, and charges inside, John yelling uselessly after him, his too tight suit clinging to his thin-ish frame, his dark curly hair blown back in the air resistance. His legs powered and he knew he wouldn't stop until he found Samantha.  
>He ran into the warehouse, looking around frantically as his eyes adjusted to the gloom, he saw the SWAT team battling with black clad men. Then he saw the man in charge- Moriarty.<br>Sherlock, overcome with grief, love, guilt, anger and sorrow all at the same moment, went flying at Moriarty, taking him out with one swoop, crying all the while, kicking until he bled several places over. Moriarty was unconscious, and at the sight of this the black clad men fled, chased by the SWAT team. That left only one figure lying on the floor, unable to move, eyes wide with terror, clothes soaked in blood, and it could be only one person, and they were very, very much alive-  
>Samantha.<br>Sherlock ran to her.


	4. Chapter 4

I lay there, soaked in my own blood. I was more than terrified. I was... Was there even a word for it? Longing for Sherlock, to put an end to whatever I had started. Sherlock. That was all I could think of.  
>And then he was there. He had simply appeared, and I didn't care how he got there because before I knew it I was clutching the back of his skin tight suit, digging my nails into his flesh to check it really was him, clutching fistfuls of his dark curly hair, burying my face into his neck, breathing in his scent, ignoring the pain in my beaten chest and reaching up to him, hugging him tight, and with no desire to let go, ever, ever, because this was Sherlock, this was my dad and I loved him so very much and a world without him would be too much to bear, even after death, even after I have departed. I smiled for the first time in days. I felt his hand on my back, clutching me to his chest, his other hand in my hair, mussing up the black mess, his chin on my shoulder, his deep, soothing voice muttering in my ear about how much he missed me and how I scared him like hell and how I can never ever do that again to him, but the words were lost as joy overcame him, overcame me, and we got lost in the moment, struggling to hold each other tighter, slipping then pulling back, and never, never letting go. Never.<br>I pulled back after a while, not because I wanted to but because I had to. My chest had started to restrict my breathing. He looked at me with an expression I had never seen before on his face. Was it... Longing? Hurt? Or... Joy.  
>"Sherlock, I-" I started, but he silenced me. Still with an expression of complete and utter happiness on his face he called Lestrade over, who had been watching us from a distance, and said:<br>"Watch Moriarty." Lestrade nodded once and obliged.  
>I wanted to hug Sherlock again. I was pretty sure he wanted to hug me too, but I had serious wounds, and before I could do anything Sherlock had called John over with a first aid kit (but a little more advanced than a few plasters) and I felt hands on the gash. Wait- two pairs of hands. Sherlock was helping.<br>I groaned in pain, twitching. It was hurting like hxell now, drowning my joy out by sending rivers of boiling pain up through my body, making me let out a single scream of agony, but then one of the hands stopped working and Sherlock was there, and the pain dulled slightly as he injected something into my arm. It was barable now, only just though. Occasional groans kept escaping my lips, and the odd yell, but I was OK. A second pair of hands set to work again.  
>Then the rivers of boiling pain came though the mist of anaesthetic, hitting me again with brute force and knocking another scream out through my lips. Then Sherlock was there again, but this time he didn't inject stuff to make the pain go away, he just sat there, holding my torso in his arms, gripping me like if I let go I would go forever and still I felt the hands inflicting pain to make me feel better.<br>I groaned loudly, letting out an 'ah' and moving my right hand up to Sherlock's shoulder. I felt like I wanted this to end, all of it, right here and right now, so that I could spend every second of my time with Sherlock. I... Needed him.  
>I screamed again. John had just found the bullet imbedded in my thigh. This was gonna hurt.<br>I screamed again, and carried on screaming, though my screams turned into 'Sherlock' and he told me to calm down and stop being silly it was just a bullet. I breath laughed at his joke, then screamed again.  
>I carried on groaning as John stitched up the rest of the gash, clearing blood, and basically doing what had to be done to save my life. I would thank him for that later.<br>Obviously I couldn't walk, and so Sherlock carried me to the van, hands gently holding me so the gash wouldn't hurt. He lay me down in the back of the van as it speeded off to get to the hospital, and my last thoughts are of being watched by Sherlock as I fell asleep.


	5. Chapter 5

I woke up to the sound of a beeping heart monitor. I opened my eyes, but only glaring white-washed walls and brutal sunlight flooded in, so I shut them again. A few seconds later I opened them again.  
>I was in a hospital bed in a private ward. The heart monitor that had woken me up was my own, and I was pretty thankful it was still beeping. There was an empty chair by my side, and a strange sticky thing attached to my arm with a tube running out of it.<br>I tried to move but a huge wave of pain washed up from my whole left side so I decided to stay where I was. There was a cord hanging by my bed so I rang it, hoping to see a nurse or doctor or someone appear.  
>A tall man with dark curly hair and a too tight suit walked in. He was around 30, straight, single but not looking for a woman. He lived in a flat with a flatmate whom he loves and trusts, but at the moment he is very worried about someone or something, and-<br>I had already deduced all this before I realised it was Sherlock. I wanted to run to him but I could barely move, the gash on my side restricticting my movements so much. But I needed to tell him something. Urgently.  
>"Sherlock!" I yelled, and he walked over to the empty chair beside my bed. He smiled, and I lay my head back down again, glad I had finally woken up.<br>"How long was I out?" I asked.  
>"Two days. But that was only because they had to gas you for surgery. You would have woken up long before now if they hadn't." he explained.<br>"What was, I mean... What happened? I can't remember. I can't remember anything." I said, and the worry of this dawned on me. Was I losing my memory?  
>"We stormed the warehouse where Moriarty was keeping you captive and managed to get you into hospital in time, after John had performed emergency surgery on you." he said quietly.<br>"Where is John?" I asked, looking around. All I saw were blindingly white walls and a few peices of complicated machinery. No John.  
>"He had to go to work." Sherlock said. I frowned at him.<br>"Shouldn't you be at work?" I asked. He shook his head.  
>"No. There is no work, and even if there was I told Lestrade to hold all the cases until you're OK again." he said and I felt guilty. Sherlock loved his work. And he had put it all of for me?<br>"What happened to Moriarty?" I asked, fragments of the warehouse scene coming back, slowly but surely. I remember lying on the ground, screaming in agony while John healed the gash... Nothing I could do, I couldn't move or barely breathe. My beaten stomach still felt painful as I lifted my chest up to breathe, short ragged breaths.  
>"He... Well, he didn't escape, he just... Well, vanished. We were holding him in a cell with no windows and the door was triple deadlock sealed, with guards guarding it 247. Nothing since." Sherlock explained which confused me. And angered me. He was saying that the man that had inflicted this... Hell on me was still loose after slipping right through our fingers? God I would personally kill Lestrade.  
>I closed my eyes for a second but instantly regretted it. I could see Moriarty standing above me, watching me scream as he finished of the gash. After a while the pain became bearable and he spoke, in his smooth, mocking voice. He spoke to me.<br>"This isn't over. When Sherlock comes to find you and heals you and locks me up this is in no way over. This is just the beginning..." the words echoed in my head, breathing down every corner of my brain, taking full control of my thoughts and filling me with terror. I snapped my eyes open, staring at Sherlock. He looked confused.  
>"It isn't over Sherlock. That's what he said. He said he knew you would lock him up and heal me but he said it wasn't over. Something's going to happen Sherlock. Something big." I muttered to him, and I slowly drifted away again as the nurse and doctor came running, yelling something about blood pressure.<p> 


	6. Chapter 6

"Moriarty is still out there." Sherlock said. I ignored him. I was too angry at them to even begin to register their existence.

"Moriarty will come after you." again I didn't say anything.

"You have to know it's-"

"For my own bloody good, right?" I roared, causing him to flinch slightly. Then the façade dropped down again and he spoke.

"Yes, for your own good. We can't have a repeat of..." his eyes glanced down to where my leg was covered in bandages. I leaned across the table towards him.

"If you try to stop me going after Moriarty because I'm a little girl, or because I'm your daughter, or because I'm the only one who has ever made the famous sociopath with no feelings and a humongous brain ever care then you are... An idiot." I whispered.

Something flickered across Sherlock's face. Annoyance? Something deeper.

"I am merely offering you help."

"Well then I decline your help." I answered. He sighed.

"Samantha, I-"

"Want to keep you safe? Wanted to make sure you didn't get hurt again? Wanted to keep you all wrapped up in cotton wool? Cause this is a first. This is the first time in my entire life you gave a damn about me, and to be honest, I still don't think you do. Moriarty hit you so you, personally, want to hit him back. And I don't think you want to take care of me. I think you just want to get Jim Moriarty back for what he did to _you._" I stormed out. Sherlock didn't shout after me.

Why was he suddenly all caring? He had never cared about me before. As I walked out of the flat I heard John yelling after me, but I didn't stop and carried on walking out onto the street. My house was a while away so I took a cab home.

_12 new voice messages._

I turned my phone off so as not to have to hear them. Obviously Lauren. Probably wondering whether my leg was better. Nope.

The house seemed cold. It was too big for one person but I needed the space. All my stuff seemed to take up every inch of space available in every single room of the house but one.

The attic.

I had never actually been up there. Never opened the door. It was cold. The whole thing was just cold. And it seemed to be leaking into the rest of the house.

I mean, anything could be up there. A dead body. A ghost. Some sort of bomb. I had always been scared of going up there, but not today.

In a blur of anger, resentment and loneliness I swung open the old, wooden door. It creaked. Just like in the horror movies. But worse.

The first thing I saw were shelves. 3, to be precise. They were empty. Well, at a first, quick glance they were empty. A small, leather-bound book sat on the lowest shelf, camouflaged in dust.

_**The Journal Of Master Sherlock Holmes**_

_**1987-1989**_

I was baffled. Why was Sherlock's journal up here? Why had he even kept a journal? But most of all was the unresistable urge to open up a read what Sherlock Holmes had written in his journal.

'''31st October, 1987.

Halloween. Of course I don't believe in such nonsense – but mother and Mycroft insisted that we at least carved a pumpkin and put it outside the house. Mycroft's cronies were coming over so I have retired to my bedroom to write this. They bore me. They practically worship Mycroft though – whenever he deduces something about something they virtually clap and give him an award. I'm clever than Mycroft. Father is always praising him but mother likes me best. I'm sure of it.

Today at school all the kids were teasing me because I had no friends. My hay fever came on at just the wrong moment and they accused me of crying. I wasn't, I swear. It's not my fault they're idiots!'''

I was grinning and laughing openly, but inside I felt guilty. This was Sherlock's. And it was private.

"You found it then. Finally." A deep voice said from behind, causing me to jump and collide with the empty shelves, nearly sending them down on me. I had dropped the book and it was lying in the dust a few feet away. He sounded annoyed, almost angry.

"Why was is up here? If you didn't want anyone to find it then you could have kept it somewhere safe instead of a room in my house where I was going to end up walking into sometime!" I retaliated, annoyed at him for being annoyed at me. It was his fault for being an idiot.

"I made sure you wouldn't go in. There was protection..."

"What? The thing that made the place cold? Sherlock, I don't believe in ghosts. You know... I fact, you don't. You don't know anything about me." I said, angry. "Why are you even here?" I spat.

"I wanted to apologise."

I was taken aback. Sherlock was apologising? Almost impossible. It has to be some sort of... Trick. Just like Sherlock.

"Why?" I asked defensively.

"Because I was an idiot."

OK, now that came as a surprise. He registered the look of complete and utter disbelief on my face, realising I didn't believe him

"No, really. I am sorry. I don't want you to think I don't care about you. Because I do." He took a deep breath. "You are my daughter, and whatever people say about me being a total sociopath with no feelings, just remember." he paused. I could see it was hard for him to admit what he was about to say.

"I love you."


	7. Chapter 7

I stood there for a minute, looking at him. This wasn't something Sherlock said everyday. To me and you, Sherlock saying 'I love you' is like a normal person saying 'You're my fucking life I love you so much I want to stay with you forever'. I was stunned. I had been utterly convinced he didn't give a damn about me, but this had changed everything.

I slowly walked over a picked up the journal, placing it carefully back on the shelf in exactly the same place. I turned to face Sherlock. There was hurt and... Love in his eyes. He wasn't lying.

"I love you too." I said quietly. He smiled, lunging forwards and giving me a massive bear hug. I was enveloped in his coat, and it seemed like it was going to literally eat me as he squeezed me so tight I found it hard to breath.

"Woah... Sherlock..." I rasped, and he let go, worried.

"What's wrong?"

"You were squishing me." I said and he laughs.

"Oh. Sorry." he steps back and smiles. There is a silence for a moment. He sighed.

"I'm still not going to let you go after Moriarty."

It felt like my heart had dropped in my chest, but I didn't retaliate. He was right. I was only 12. I wasn't strong enough to fight him.

And on that note, he led me out of the attic and into whatever adventures, pain, fun and pure life that lay ahead.

**A/N: That's this story wrapped up. Thank you for all the reviews, favourites and follows. This has been a very, very deep story and I'm thank you all for following the line of dear Samantha. Goodbye:)**


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